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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGATCTTGAGAACTTTGTTGTCGAAAGAGAAAACAGAGAATCTTGATTTCCATGAGCTTGGGCAGATAACAGAAGGCTACAGTGGAAGTGATCTCAAGgtctgtgtcttctctaaccataaccaaagactgtcgtgtaaaatcgttggaaactgactgtttgttgaacttttgtacaaacag

Basic information

species Arabidopsis thaliana
transcript AT5G52882.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G52882.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GRMZM2G159307_T01 (Zea mays), 5'ss of exon 12
GAAGATCTTGAGAACTTTGTTGTCGAAAGAGAAAACAGAGAATCTTGATTTCCATGAGCTTGGGCAGATAACAGAAGGCTACAGTGGAAGTGATCTCAAGgtctgtgtc-----ttctctaaccataaccaaagactgtcgtgtaaaatcgttggaaactgactgtttgttgaacttttgtacaaacag--------------------------------
 |  ||   | ||  | |||    | |  |       || |  ||  | ||| | ||||| |     || |||||||| || ||||||||||||||||||||| ||  |      |||| |   ||       ||   | |||||| |  | ||   |  |  ||| |   |||||   ||| | |                                   
CATAATGCGGCGACTTCTGTCAAAGGAGAAAGTTGATGAAAGGCTGAACTTCAAGGAGCTAGCAACCATGACAGAAGGATATAGTGGAAGTGATCTCAAGgtcagtaacatgaactctcgatttattttttctgagaat-gtgtaagagagctgtgtatcg-ttgtattgagaactaaagtagagatcaattctgctcgatcctgaattcttctttaacag

upper sequence: AT5G52882.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GRMZM2G058491_T01 (Zea mays), 5'ss of exon 12
GAAGATCTTGAGAACTTTGTTGTCGAAAGAGAAAACAGAGAATCTTGATTTCCATGAGCTTGGGCAGATAACAGAAGGCTACAGTGGAAGTGATCTCAAGgtctgtgtcttc---tctaaccataaccaaagactgtcgtgtaaaatcgttggaaactgactgtttgttgaacttttgtacaaacag---------------------------------------------------------------------------------
 |  ||   | ||  | |||    | |  |       ||    || || ||| | ||||| |     || |||||||| || ||||||||||||||||||||| ||  | |      | |       || |  |   | || |||| |   || | |   ||       ||  | || | |  | |                                                                                  
CATAATGCGGCGACTTCTGTCAAAGGAGAAAGTTGATGAAGGGCTGGACTTCAAGGAGCTAGCAACCATGACAGAAGGATATAGTGGAAGTGATCTCAAGgtcagtagcatgaaacatgaatgcgcacacatgcccccatgaaaaa-caaaggcaccatgctcaacaccgatttatttttctgagaatacgcaagatagttgtgtatctctgtattaagagctaaagtagagatcaattatgctcgacactgaattcttctttaacag
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|125237387|gb|EL251472.1|EL251472
EST:     ATAACAGAAGGCTACAGTGGAAGTGATCTCAAG                         AACTTATGCATCACAGCTGCTTATAGACCAGTTAGAGAGCTGATTCAGCAG
genomic: ATAACAGAAGGCTACAGTGGAAGTGATCTCAAGgtctgtgtct ... gtacaaacagAACTTATGCATCACAGCTGCTTATAGACCAGTTAGAGAGCTGATTCAGCAG
EST: gi|124975888|gb|EL049347.1|EL049347
EST:     CCATGAGCTTGGGTCAGATAACAGAAGGCTACAGTGGAAGTGATCTCAAG                         AACTTATGCATCACAGCTGCTTATAG
genomic: CCATGAGCTTGGG-CAGATAACAGAAGGCTACAGTGGAAGTGATCTCAAGgtctgtgtct ... gtacaaacagAACTTATGCATCACAGCTGCTTATAG
EST: gi|124762782|gb|EH852912.1|EH852912
EST:     CTTGGGCAGATAACAGAAGGCTACAGTGGAAGTGATCTCAAG                         AACTTATGCATCACAGCTGCTTATAGACCAGTTAGAGAGCT
genomic: CTTGGGCAGATAACAGAAGGCTACAGTGGAAGTGATCTCAAGgtctgtgtct ... gtacaaacagAACTTATGCATCACAGCTGCTTATAGACCAGTTAGAGAGCT

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGATCTTGAGAACTTTGTTGTCGAAAGAGAAAACAGAGAATCTTGATTTCCATGAGCTTGGGCAGATAACAGAAGGCTACAGTGGAAGTGATCTCAAGgtctgtgtcttctctaaccataaccaaagactgtcgtgtaaaatcgttggaaactgactgtttgttgaacttttgtacaaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG